Focusing Screen out-of-focus-to-focus "Phenomenon"; A pickle revisited!

Because the focusing screens aren't truly matte, the diopter setting slightly affects where you judge the best focus setting to be, in my experience. The image itself is moving up and down within the focusing screen. If they were truly matte, it wouldn't affect that at all.

Note that the AF boxes are on a separate plane closer to you than the focusing screen. What happened for you is that the best diopter setting for accurate focusing seems to be somewhat farther away than normal, making it hard for your eye to focus on the image in the focusing screen and the AF boxes at the same time.